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Between 70 and 100 "experienced" staff have left the system since 2011, union spokesman Andrew Capp said.

"A lot left because they felt persecuted," he told a parliamentary inquiry into youth justice centres on Tuesday.

The CPSU also revealed it has a secret government report by consultant Peter Muir.

The Muir report was commissioned after March 2016 riots at Parkville's Melbourne Youth Justice Centre and handed to the government in May the same year.

It warned of deep dysfunction and more riots, according to a leaked copy reported by Fairfax media.

The CPSU said it received a copy of the report from the government as part of consultation with the sector - but parliament has never received a copy, prompting scoffs from Liberal MPs during the inquiry.

Six months after the report was handed over, Parkville detainees went on a rampage in November, rendering parts of the centre uninhabitable.

As a result, the government to moved youths into the adult Barwon prison sparking a series of legal challenges.

In a separate inquiry, the minister responsible for the sector faced questioning over her handling of the portfolio.

Youth Affairs Minister Jenny Mikakos and top bureaucrats were unable to tell a budget estimates committee on Tuesday how much the government had spent defending the three failed court cases over the Barwon teens.

"It seems incredible to me that we have a court case that has been concluded and you can't tell me what it cost," opposition MP David Morris told the committee.